1. Pipelines, Data Transfer, and Reconstructions
Rick Herrick
13 Sept, 2012

2. Who’s back from the 2010 workshop?
Who’s been using XNAT for a while?
Who’s a complete and utter novice?
Pipelines
We currently support only the XNAT pipeline engine out of the box
Relatively easy to customize execution parameters to allow integration of other engines (e.g. nipype)
Very powerful and flexible: if you can run it, it can be part of your pipeline
Driven by configuration files and integrated and launched through the GUI (mostly)

3. Let's see it then Pipeline definition Catalog entry
Add the pipeline to the system
Attach the pipeline to a project
We'll run it a little bit later...

4. Uploading data The single most important function in the system!
DICOM C-STORE SCP
Direct from scanner
DICOM Browser
Other tools like OsiriX
Upload Applet
Inline anonymization
DICOM attribute validation before upload
Zip Uploader
REST API

5. Uploading data, continued...
XNAT provides a review workflow for image upload:
Incoming data goes into the prearchive
Allows for complete receive
Review session before archiving
DICOM attribute validation before upload
Inline anonymization
Zip Uploader
REST API

6. Moving into the Archive
The archive is where sessions become permanent:
Auto-run pipeline
Snapshot generation
Automated QC
Format conversion
Manual QC
Image assessors
Reconstructions
Associated with a subject!

7. Image Reconstructions
A reconstruction is a transformation or extrapolation from existing source data:
Format conversion (e.g. DICOM to NIFTI)
Freesurfer
FSL
4dfp
3D Slicer
...

8. Bring It All Together... Add pipelines to the project: Validation
DicomToNifti
Configure the pipeline launch page for data type
Run the validation pipeline
Check the results
Run the DicomToNifti pipeline
AutoRun pipeline

9. Q&A